The role of chromatin structure in modulating the functions of DNA in transcription, replication, recombination and repair is becoming increasingly apparent. We have shown that the yeast alpha2 repressor positions a nucleosome adjacent to its operator. This organized chromatin structure is propagated; at least three additional nucleosomes are positioned with base pair precision. This structure seems to be the mechanism of repression; mutations in several yeast genes whose function is known to be necessary for repression by alpha2 also lead to perturbation of the organized chromatin structure. Studies moving the transcription initiation site relative to the alpha2 operator demonstrate that repression is involved with chromatin structure above the level of an individual nucleosome. In the case of one haploid specific gene, an organized chromatin structure is found near an a1/alpha2 binding site in diploids. Hierarchies exist in the contest between transcription factors and histones. While alpha2 can organize chromatin structure and repress transcription of a-cell specific genes, the GAL4 protein can bind to its operator, disrupting formation of a stable nucleosome. A systematic study of the use of prokaryotic dam methylase for probing chromatin structure has defined the accessibility of nucleosomal, linker, and hypersensitive region DNA to the modifying protein. Studies of the expression of the sporulation induced HSP82 gene have defined elements that are necessary for normal expression, although likely not for meiosis responsiveness, and an apparent repressor sequence. Collaborative studies of higher order chromatin structure and the crystal structure of a nucleosome core particle containing unique sequence DNA continue.